Miruna GT Chick Velocity Custom Plotting

Extract velo matrices and gene info from adata

python3 ../src/pull_velo_info.py

R load

suppressPackageStartupMessages({
    library("tidyverse")
    library("reticulate")
    library("ggplot2")
    library("SingleCellExperiment")
    library("scater")
    library("Seurat")
    library("SeuratDisk")
    library("zellkonverter")
})
# load('~/data/chick_miruna/08052021.RData')
# save just combined to reduce load time from Miruna's entire environment
# save(combined, file = '~/data/chick_miruna/combined_mgg_08052021.Rdata' )
load('~/data/chick_miruna/combined_mgg_08052021.Rdata')
combined

An object of class Seurat 
20555 features across 17295 samples within 2 assays 
Active assay: RNA (18555 features, 0 variable features)
 1 other assay present: integrated
 2 dimensional reductions calculated: pca, umap

color_palette <- pals::glasbey()[1:14]
names(color_palette) <- seq(0,13, 1)

Build Labelled Matrix

Plots

genes <- c("NTRK3", "REEP5", "RBP3", "THRB", "MEIS2", "PRDM1", "ONECUT1", "TOX3", "SIX6", "OTX2", "FGFR3",  "TFAP2E")
for (i in genes){
  print( velo_scale_df %>% filter(Gene == i) %>%  ggplot(aes(x=UMAP_1, y = UMAP_2, color = Velocity)) + 
           geom_point(size = 0.3) +  
           cowplot::theme_cowplot() + scale_color_gradient2(
             low = "green", 
             high = "blue", 
             mid = 'gray'
           ) + 
           facet_wrap(~cluster.condition) + 
           ggtitle(i)
  )
}

devtools::session_info()

─ Session info ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.1.2 (2021-11-01)
 os       macOS Catalina 10.15.7
 system   x86_64, darwin17.0
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       America/New_York
 date     2022-05-16
 rstudio  2021.09.0+351 Ghost Orchid (desktop)
 pandoc   2.14.0.3 @ /Applications/RStudio.app/Contents/MacOS/pandoc/ (via rmarkdown)

─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
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 [1] /Users/mcgaugheyd/git/chick_analysis_collab/renv/library/R-4.1/x86_64-apple-darwin17.0
 [2] /Library/Frameworks/R.framework/Versions/4.1/Resources/library

 P ── Loaded and on-disk path mismatch.

─ Python configuration ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 python:         /Users/mcgaugheyd/git/chick_analysis_collab/renv/python/virtualenvs/renv-python-3.9/bin/python
 libpython:      /usr/local/opt/python@3.9/Frameworks/Python.framework/Versions/3.9/lib/python3.9/config-3.9-darwin/libpython3.9.dylib
 pythonhome:     /Users/mcgaugheyd/git/chick_analysis_collab/renv/python/virtualenvs/renv-python-3.9:/Users/mcgaugheyd/git/chick_analysis_collab/renv/python/virtualenvs/renv-python-3.9
 version:        3.9.4 (default, Apr  5 2021, 01:49:30)  [Clang 12.0.0 (clang-1200.0.32.29)]
 numpy:          /Users/mcgaugheyd/git/chick_analysis_collab/renv/python/virtualenvs/renv-python-3.9/lib/python3.9/site-packages/numpy
 numpy_version:  1.21.5
 
 NOTE: Python version was forced by RETICULATE_PYTHON

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